Parallel Discrete Event Simulation of Molecular Dynamics Through Event-Based Decomposition

  • Authors:

  • Martin C. Herbordt;Md. Ashfaquzzaman Khan;Tony Dean

  • Affiliations:

  • -;-;-

  • Venue:
  • ASAP '09 Proceedings of the 2009 20th IEEE International Conference on Application-specific Systems, Architectures and Processors
  • Year:
  • 2009

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Abstract

Molecular dynamics simulation based on discrete event simulation (DMD) is emerging as an alternative to time-step driven molecular dynamics (MD).DMD uses simplified discretized models, enabling simulations to be advanced by event, with a resulting performance increase of several orders of magnitude.Even so, DMD is compute bound.Moreover, unlike MD, causality issues make DMD difficult to scale.Here we present a microarchitecture-inspired parallel algorithm for DMD:speculative execution enables multithreading, while in-order commitment ensures correctness.Our initial not-yet optimized implementation obtains scalability for a multicore processor when running realistic simulation models.